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University of California Davis Researchers Discover Infant Microbiomes Lack B. Infantis in Developed Nations

Without the beneficial bacteria, infants can develop gut dysbiosis, which can lead to severe chronic diseases

Another key insight into how the human microbiome performs essential functions has been discovered by a research team at the University of California, Davis (UCD). They have learned that nearly all babies born in developed nations no longer have a specific strain of bacteria called B. infantis, which digests a certain type of sugar found in breast milk.

Microbiologists, clinical laboratory scientist, and pathologists will find the UCD researcher’s discovery to be a fascinating insight into a newly-understood function of the human microbiome. Assuming that further research confirms these early findings, it also could lead to a medical laboratory assay for use during pregnancy or after delivery that would enable physicians to determine if the newborn is missing this strain of bacteria and what therapies would be appropriate.

Babies in Developed Nations Lack Beneficial B. infantis Bacteria

“The central benefits of having a microbiota dominated by B. infantis is that it crowds all the other guys out—especially pathogenic bacteria, which can cause both acute illnesses and chronic inflammation that leads to disease,” UC Davis researcher Bruce German, PhD, Professor and Chemist, Food Science and Technology, told the New York Times.

The UC Davis researchers published their study findings in mSphere, a journal of the American Society for Microbiology. In their paper they note that Bifidobacterium Infantis or B. infantis, a beneficial bacteria that aids in digestion, is missing from the microbiomes of infants in developed nations, such as the United States.

The study hypothesized that the reduction and eventual absence of B. infantis in American babies was the consequence of three factors:

  • An increase in cesarean births;
  • Use of commercial formulas instead of breast milk; and,
  • Heightened use of antibiotics.

According to the New York Times, “Dr. German and his colleagues learned about the missing bacterium by studying breast milk. They found that the milk contains an abundance of oligosaccharides, carbohydrates that babies are incapable of digesting. Why would they be there if babies can’t digest them? They realized that these carbohydrates weren’t feeding the baby—they were feeding B. infantis.”

Good versus Bad Gut Bacteria

Because 70-80% of our immune system resides within our gastrointestinal tract, gut bacteria play an important role in our overall health. Breast milk contains essential probiotics and anti-inflammatory compounds that help “friendly” bacteria flourish in the infant gut.

There are more than two hundred different sugars or carbohydrates found in breast milk, known as human milk oligosaccharides (HMOs). They are one of the most copious components in breast milk but are completely indigestible by humans. So, why are they there?

Because they serve a critical role as food for microbes or prebiotics. Scientists have discovered that HMOs present in breast milk are there to feed the B. infantis, not to nourish the baby.

HMOs also act as a decoy to confuse undesirable bacteria from doing damage in the gut.

“Bad” bacteria are inclined to latch onto sugar molecules in intestinal cells. Because HMOs are very similar to those sugar molecules, the undesirable bacteria will instead latch onto the HMOs in a baby’s gut and leave vulnerable intestinal cells alone.

The primary benefits of B. infantis include:

  • Production of short-chain fatty acids. When infantis digests HMOs, some short-chain fatty acids are released, which provide energy and help control yeast and fungus growth.
  • Support for gut integrity. infantis signals gut cells in infants to generate proteins that fill gaps between intestinal cells. These gaps can be dangerous as they may allow toxins and bad bacteria to get into the bloodstream.
  • Keeping undesirable bacteria at bay. infantis consumes HMOs and usurps space in the gut so potentially dangerous bacteria cannot take up residence or cause problems.
  • Release of sialic acid. As it devours HMOs, infantis churns and releases sialic acid, a crucial nutrient for the brain development of infants.
  • Production of folate. infantis also produces folate, which is necessary for infant development and growth and the creation of red blood cells.

“The need for clinicians to have a quick and reliable method to determine Bifidobacterium levels in [a] baby’s gut, and an effective way to replace the right Bifidobacterium to correct dysbiosis when detected, are the critical next steps for infant health,” noted Jennifer Smilowitz, PhD (above), Associate Director of Human Studies Research Program for the Foods for Health Institute at UC Davis, and one of the study authors, in a news release. (Photo copyright: UC Davis.)

Alarming Changes to Infant Gut Microbiome

The UC Davis study is the latest example of new insights about the microbiome, which refers to the collected genetic material of human microbiota. This promising field of research is expected to lead to a better understanding of how human gut bacteria affects resistance to certain chronic diseases, such as cancer, and to new clinical laboratory treatments and drug therapies.

Different research initiatives involving the human microbiome continue to indicate that gut bacteria can be a source of useful biomarkers for improving the health of individuals. Dark Daily has covered the study of human microbiome and development of new cancer therapies based on that research for many years.

Microbiome research, however, sometimes uncovers negative findings as well.

Lack of B. infantis, a principle gut microbe, can contribute to gut dysbiosis, which has been linked to chronic health conditions such as:

Researchers observed that reduction in B. infantis in the infant gut also has resulted in a rise in the pH of infant fecal matter. An analysis of 14 clinical studies performed between 1926 and 2017 showed a startling increase of pH from 5.0 to 6.5 in infant stools.

“These alarming changes to the infant gut microbiome and thus, gut environment, may be due to modern medical practices like antibiotics, C-sections, and formula feeding,” Jennifer Smilowitz, PhD, Associate Director of Human Studies Research Program for the Foods for Health Institute at UC Davis, and one of the study authors, noted in a news release. “These are all potentially life-saving medical practices but have unintended consequences on the infant gut microbiome. As a result, certain pathogenic bacteria—those linked to higher risk of health issues, such as colic, eczema, allergies, diabetes, and obesity—thrive.”

The process by which the researchers in this study identified the missing bacteria illustrates how more refined ways to examine molecules in the body are providing streamlined tools to identify elements within the body and their interaction with each other.

This new insight is one more confirmation that the human microbiome will be the source of useful diagnostic biomarkers, associated with medical laboratory therapies that can improve the health of individual patients.

—JP Schlingman

Related Information:

Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century

The Bacteria Babies Need

Bifidobacterium Longum Subspecies Infantis: Champion Colonizer of the Infant Gut

Evolve BioSystems’ Activated B. infantis EVC001 Demonstrates Substantial and Persistent Remodeling of the Infant Gut Microbiome

How Baby’s First Microbes Could be Crucial to Future Health

Breast Milk and B. Infantis: Nature’s Favorite Probiotic

New Study Shows Significant Changes to Infant Fecal pH Over Last 100 Years

Researchers Discover Link between Gut Bacteria and the Effectiveness of Certain Cancer Drugs; Knowledge May Lead to New Types of Clinical Laboratory Tests

Researchers in Two Separate Studies Discover Gut Microbiome Can Affect Efficacy of Certain Cancer Drugs; Will Findings Lead to a New Clinical Laboratory Test?

Microbiologists at Weill Cornell Use Next-Generation Gene Sequencing to Map the Microbiome of New York City Subways

University of Illinois Study Concludes Regular Physical Exercise Improves Human Microbiome; Might Be Useful Component of New Treatment Regimens for Cancer and Other Chronic Diseases

Exercise contributes to improving the human microbiome in ways that fight disease and clinical labs might eventually provide tests that help track beneficial changes in a patient’s microbiome

With growing regularity, new discoveries about the human Microbiome have been reported in scientific journals and the media. Some of these discoveries have led to innovations in clinical laboratory tests over the past few years. Dark Daily reported on these breakthroughs, which include: improved cancer drugs, life extension, personalized medical treatments (AKA, precision medicine), genetic databases, and women’s health.

Now, a study from the University of Illinois at Urbana-Champaign (UI) has linked exercise to beneficial changes in the makeup of human microbiota. The researchers identified significant differences in the gut bacteria of obese and lean individuals who underwent the same endurance training. The lean individuals developed healthy gut bacteria at a much higher rate than the obese participants. And they retained it, so long as the exercise continued.

Thus, researchers believe weight loss and regular exercise could become critical components of new treatment regimens for many chronic diseases, including cancer.

Regular Exercise Increases Good Gut Bacteria in Humans and Mice

The UI researchers published the results of their study in Medicine and Science in Sports and Exercise, a journal of the American College of Sports Medicine. To perform their study, they analyzed the impact six weeks of endurance training had on the gut bacteria of 32 adults:

  • Eighteen of the subjects were lean and the remaining 14 were obese;
  • Eleven of the obese and nine of the lean participants were female; and,
  • All 32 were sedentary before the study began.

The subjects participated in six weeks of supervised exercise three days/week. They started at 30-minutes/day and progressed to 60-minutes/day. Fecal samples were collected from the participants before and after the six weeks of training. The subjects were instructed to not change any of their dietary habits during the study.

Upon completion of the initial six-week exercise program, participants returned to a sedentary lifestyle for another six weeks and then researchers took more fecal samples.

Jacob Allen, PhD-Candidate (left), and Jeffrey Woods, PhD

In a University of Illinois study, Jacob Allen, PhD-Candidate (left), and Jeffrey Woods, PhD (right), et al, concluded that regular exercise increased production of beneficial gut bacterial (microbiome) more in lean individuals than in obese participants. This finding could alter how anatomic pathologists and medical laboratories view exercise and weight loss for patients undergoing treatment regimens for chronic diseases. (Photo copyright: University of Illinois/L. Brian Stauffer.)

As a result of the study, the researchers found the gut bacteria of the subjects did change, however, those changes varied among the participants. Fecal concentrations of short chain fatty acids (SCFAs), particularly butyrate, increased in the guts of the lean participants but not in the guts of the obese subjects.

SCFAs have been shown to improve metabolism and reduce inflammation in the body, and they are the main source of energy for the cells lining the colon. However, nearly all of the beneficial changes in the participants’ gut bacteria disappeared after six weeks of non-exercise.

“The bottom line is that there are clear differences in how the microbiome of somebody who is obese versus somebody who is lean responds to exercise,” Jeffrey Woods, PhD, Professor, Department of Kinesiology and Community Health, College of Applied Health Sciences, University of Illinois at Urbana-Champaign and co-leader of the study, told UI’s News Bureau. “These are the first studies to show that exercise can have an effect on your gut independent of diet or other factors.”

Reduced Inflammation Promotes Healing

The researchers had previously performed a related study using lab mice and found similar results. For that experiment, mice were separated into two groups where some were permitted to run around and be active while the others were sedentary. The gut material from all of the mice was then transplanted into gnotobiotic (germ-free) mice where their microbiomes were exposed to a substance that was known to cause irritation and inflammation in the colon. The animals with the gut bugs from the active mice experienced less inflammation and were better than the sedentary mice at resisting and healing tissue damage.

“We found that the animals that received the exercised microbiota had an attenuated response to a colitis-inducing chemical,” Jacob Allen, PhD Candidate, co-leader of the study and former doctoral student at UI, now a postdoctoral researcher at Nationwide Children’s Hospital in Columbus, Ohio, told the UI News Bureau. “There was a reduction in inflammation and an increase in the regenerative molecules that promote a faster recovery.”

Exercise Added to Growing List of Benefits from Health Gut Bacteria

Similar research in the past has found that healthy gut bacteria may have many positive effects on the body, including:

  • Improved immune health;
  • Improved mood and mental health;
  • Boosting energy levels;
  • Improved cholesterol levels;
  • Regulated hormone levels;
  • Reduction of yeast infections;
  • Healthy weight support;
  • Improved oral health; and,
  • Increased life expectancy.

Other ways to improve gut bacteria include: dietary changes, taking probiotics, lowering stress levels, and getting enough sleep. Now regular exercise can be added to this growing list.

Once further research confirms the findings of this study and useful therapies are developed from this knowledge, clinical laboratories should be able to provide microbiome testing that would help physicians and patients track the benefits of exercise on enhancing gut bacteria.

—JP Schlingman

Related Information:

Exercise Alters Our Microbiome. Is That One Reason It’s So Good for Us?

Exercise Training-induced Modification of the Gut Microbiota Persists After Microbiota Colonization and Attenuates the Response to Chemically-induced Colitis in Gnotobiotic Mice

Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans

Exercise Changes Gut Microbial Composition Independent of Diet, Team Reports

Exercise Can Beneficially Alter the Composition of Your Gut Microbiome

Researchers Discover Link between Gut Bacteria and the Effectiveness of Certain Cancer Drugs; Knowledge May Lead to New Types of Clinical Laboratory Tests

Researchers in Two Separate Studies Discover Gut Microbiome Can Affect Efficacy of Certain Cancer Drugs; Will Findings Lead to a New Clinical Laboratory Test?

Attention Microbiologists and Medical Laboratory Scientists: New Research Suggests an Organism’s Microbiome Might Be a Factor in Longer, More Active Lives

Get the Poop on Organisms Living in Your Gut with a New Consumer Laboratory Test Offered by American Gut and uBiome

Mayo Clinic and Whole Biome Announce Collaboration to Research the Role of the Human Microbiome in Women’s Diseases Using Unique Medical Laboratory Tests